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11593 Commits
Author SHA1 Message Date
John Chilton d657855b7f Remove unused test_conf variable. 2016-03-29 08:04:25 -04:00
John Chilton 33d312b906 [16.01] Fix for running jobs when metadata tool is not in toolbox. 
Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config.
 2016-03-29 08:04:25 -04:00
Björn Grüning ad12042f5f Merge pull request #2025 from jmchilton/ts_tool_data_table_config 
Don't setup a default tool_data_table_config_path in the shed.
 2016-03-29 06:22:28 +02:00
Bjoern Gruening 1be896fd15 data_column to json config file 2016-03-29 00:36:19 +02:00
John Chilton a9d51f6dfe Don't setup a default tool_data_table_config_path in the TS. 2016-03-28 16:53:12 -04:00
guerler 207af3d975 Fix multiple flag for workflow dataset inputs 2016-03-27 23:48:15 -04:00
Martin Cech c093c793b7 Merge pull request #1958 from jmchilton/workflow_scheduling_testing 
Improvements to workflow scaling performance testing scripts.
 2016-03-25 22:32:28 -04:00
guerler 1423836f1e Fix collection handling 2016-03-25 13:39:51 -04:00
Dannon Baker 0d5001eea7 Merge branch 'release_16.01' into dev 2016-03-25 11:11:26 -04:00
John Chilton ec3fe67ddd Merge pull request #1918 from davebx/move_tsg 
Rename tool_shed_get to url_get.
 2016-03-25 10:57:03 -04:00
John Chilton 6e34858e0d Merge pull request #2010 from guerler/fix_collection_select 
Fix parameter expansion for empty collections
 2016-03-25 10:54:33 -04:00
John Chilton 84044f9a5f Merge pull request #2002 from dannon/statswork 
Much more friendly route mapping.
 2016-03-25 10:53:48 -04:00
John Chilton 86d2b29026 Merge pull request #1993 from guerler/revise_parameters_000 
Fix inconsistency in update state handling for tool modules
 2016-03-24 16:39:26 -04:00
guerler 72b1ba3714 Fix parameter expansion for empty collections 2016-03-24 16:29:13 -04:00
John Chilton dc49a9cbc1 Fix unbound error that is possible if using tool bursting. 2016-03-24 14:35:51 +00:00
guerler eaf8f4ed50 Extend doc tests for parameter handling 2016-03-23 16:20:51 -04:00
guerler c1fe8aac0a Fix inconsistency in update state handling for tool modules 2016-03-23 14:28:07 -04:00
Dannon Baker 033241c99f Merge 16.01, rebuild. 2016-03-23 12:39:06 -04:00
Martin Cech 21e71a9b46 Merge pull request #1905 from dannon/library_errors 
[16.01] Encoding in libraries
 2016-03-23 12:04:27 -04:00
Dave Bouvier 7e14f5db62 Address travis' complaints. 2016-03-23 11:40:20 -04:00
guerler 946458b892 Fix booleans 2016-03-23 11:09:43 -04:00
Dave Bouvier 06b9737e09 Cleanup and fix tests. 2016-03-23 10:04:26 -04:00
Dave Bouvier 9e8890b25b Merge branch 'dev' of git://github.com/galaxyproject/galaxy into move_tsg 2016-03-23 09:54:08 -04:00
Dannon Baker 975c6f5eae Much more friendly route mapping. 2016-03-22 17:35:14 -04:00
Nicola Soranzo d10ee6f6c4 Merge branch 'release_16.01' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-03-22 20:54:32 +00:00
Nicola Soranzo 9eb1db82ca Do not convert spaces to tabs when importing datasets into a library. 
Reported (with fix provided) by Fabien Mareuil in
http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-header-td4669160.html
 2016-03-22 20:03:32 +00:00
Dannon Baker 0dc57b08e8 Merge pull request #1974 from jmchilton/docker_fix 
Fix docker tool execution for #1688.
 2016-03-22 12:42:16 -04:00
Dannon Baker 45c1731888 Merge branch 'release_16.01' into dev 2016-03-22 09:18:55 -04:00
Björn Grüning 30750c32e4 Merge pull request #1880 from dannon/fix_migration_0131_mysql 
[16.01] Fixes to subworkflow migration 0131
 2016-03-22 14:14:43 +01:00
John Chilton 55e8ef6e1d Optimize adding datasets to large histories. 2016-03-22 13:12:15 +00:00
John Chilton c26788a267 Merge pull request #1971 from guerler/fix_nginx_upload_000 
Fix nginx-based file upload
 2016-03-22 07:51:33 -04:00
John Chilton 975937ec9d Fix docker tool execution for #1688. 
Thanks for @kellrott for the bug report.

\#minor
 2016-03-22 10:02:32 +00:00
guerler 4e3ca993f2 Fix nginx-based file upload 2016-03-21 20:44:22 -04:00
Dannon Baker 35e75d11ce Merge branch 'release_16.01' into dev. 
Rebuild client.
 2016-03-21 19:33:05 -04:00
Dannon Baker 566f556b07 Merge pull request #1952 from guerler/fix_tool_access_000 
[16.01] Fix tool access rights and forwarding
 2016-03-21 19:29:31 -04:00
Dannon Baker 8d37aeff50 Manual merge to resolve conflict 16.01->dev 2016-03-21 16:36:48 -04:00
Dannon Baker 377ccbe23b Merge pull request #1967 from jmchilton/fix_optional_numeric_params 
[16.01] Fix #1721.
 2016-03-21 16:18:27 -04:00
John Chilton 2efd9c2687 Fix #1721. 
TODO: write test...
 2016-03-21 13:51:26 +00:00
John Chilton 5df7830424 Do not use "is not" to compare strings. 
http://stackoverflow.com/questions/1504717/why-does-comparing-strings-in-python-using-either-or-is-sometimes-produce
 2016-03-21 12:06:35 +00:00
John Chilton 5ead8a95d1 Merge pull request #1941 from bgruening/chemical_datatypes 
add chemical datatypes
 2016-03-21 11:49:31 -04:00
John Chilton c8cb4280c1 Fix datatype sniff test to use sample and revert molecule registry hacks. 2016-03-21 09:53:21 +00:00
John Chilton 85ef86ab2e Improvements to workflow scaling performance testing scripts. 
- Implement a wrapper script for launching a docker-galaxy-stable setup a many ways for this task including:
    - Configure container's Galaxy with outer Galaxy's lib and test directory.
    - Collect log files.
    - Log a statement for interacting with the container easily while the test is running.
    - Disable unneeded services.
 - Implement a fan-in-fan-out style workflow for performance testing.
 - Add an option to test performance of scheduling workflows without actually running jobs.
 - Sample tool for creating large collections easily at beginning of tests (much faster than uploads).
 - Sample tool for splitting a file into a collection for fan in and out workflow test.
 - Assume Python 2.7 in scripts to simplify things.
 - Add documentation.
 2016-03-21 01:39:45 +00:00
John Chilton 09a0e9395d More job related timing logging. 
- Log time of big flush statement.
 - Log time of adding datasets to history.
 - Log time for setting up job.

These log statements would make the output of the following gist (https://gist.github.com/blankenberg/43db2e0f61a566126c45) from #1831 a lot more informative.
 2016-03-21 01:03:25 +00:00
John Chilton 9e9dfdfd55 Fix workflow scheduler log message. 2016-03-21 00:51:18 +00:00
Bjoern Gruening 1e9b0e6dbd add molecule datatypes, like PDB and some cheminformatic ones 2016-03-20 18:06:14 +01:00
Martin Cech d0ceb29bd8 Merge pull request #1953 from mvdbeek/warn_if_user_inactive 
Warn if tool is executed and user account is inactive
 2016-03-20 11:40:52 -04:00
Marius van den Beek 34dedb3eb9 linting fixes 2016-03-20 12:04:33 +01:00
Marius van den Beek 3b71020dfc Account for anonymous user. 2016-03-20 11:49:21 +01:00
Marius van den Beek 9d362a2400 log warning if user account is not active 2016-03-20 10:24:37 +01:00
guerler 054fdf76f0 Parse user when filtering tools 2016-03-18 20:48:24 -04:00